STAT 555 - Statistical Analysis of Genomics Data

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course overview

The course is dedicated to statistical and computational methods for the design and analysis of bioinformatics experiments.

course topics

The topics that will be covered in this course will likely include:

  1. Introduction to R and RStudio
  2. Introduction to cell biology
  3. Introduction to measurement technologies: microarrays, sequencing, SNPs and ChIP
  4. Basic statistics
  5. Gene Expression Microarrays: experimental designs, preprocessing and normalization, differential expression.
  6. RNA-seq: experimental designs, preprocessing and normalization, differential expression, splice variants
  7. SNPs
  8. ChIPs
  9. Replication and pooling
  10. Gene Set enrichment analysis
  11. Clustering samples and genes
  12. Classifying samples using statistical machine learning
  13. Dimension reduction
  14. Combining data from multiple platforms
  15. Selected topics such as gene networks, time course experiments and project presentations as time permits

Here is a link to the Online Notes for STAT 555.

prerequisites

The course has no pre-requisites, but some computational skills and/or familiarity with basic concepts in statistics, bioinformatics and/or cell biology will help. Undergraduates must obtain consent of the instructors to register for the course.

textbook

There will be no required text-book. Online course materials will combine methodological background description and presentation of analyses and results from recent articles. References and notes will be posted.

software

This course makes extensive use if the R statistical software. See the Department of Statistics' Statistical Software page for information about obtaining a copy of R.

assessment plan

  • 4 - 6 Homework Assignment (50% of grade)
  • Individual Project and Presentation (50% of grade)

academic integrity

All Penn State policies regarding ethics and honorable behavior apply to this course. Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this institution. All University policies regarding academic integrity apply to this course. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students.

For any material or ideas obtained from other sources, such as the text or things you see on the web, in the library, etc., a source reference must be given. Direct quotes from any source must be identified as such.

All exam answers must be your own, and you must not provide any assistance to other students during exams. Any instances of academic dishonesty WILL be pursued under the University and Eberly College of Science regulations concerning academic integrity. For more information on academic integrity, see Penn State's statement on plagiarism and academic dishonesty.

The Eberly College of Science Code of Mutual Respect and Cooperation embodies the values that we hope our faculty, staff, and students possess and will endorse to make The Eberly College of Science a place where every individual feels respected and valued, as well as challenged and rewarded.

disabilities

Penn State welcomes students with disabilities into the University's educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact the Office for Disability Services (ODS) at 814-863-1807 (V/TTY). For further information regarding ODS, please visit the Office for Disability Services Web site at http://equity.psu.edu/ods/.

In order to receive consideration for course accommodations, you must contact ODS and provide documentation (see the documentation guidelines at http://equity.psu.edu/ods/guidelines/documentation-guidelines). If the documentation supports the need for academic adjustments, ODS will provide a letter identifying appropriate academic adjustments. Please share this letter and discuss the adjustments with your instructor as early in the course as possible. You must contact ODS and request academic adjustment letters at the beginning of each semester.

course author

Dr. Naomi Altman is the primary author of these course materials.